Dear Gromacs users,
I am analyzing the RMSD evolution of a trajectory with g_rms and
clustering it with g_cluster (GROMOS, cutoff 0.1). I am noticing
something quite odd in the RMSD distribution. I link here the RMSD
evolution over time , the cluster ID over time, and the RMSD
distribution (see http://imgur.com/a/0ftA2 ).
RMSD evolution in time and cluster ID in time seem to make sense -the
larger cluster is cluster 1, and it indeed populates most of the
trajectory.
The RMSD distribution is also correctly bimodal and peaked around the
right values, at least visually. However, I would expect that the peak
around 0.3-0.4 should be larger than the peak around 0.1, given the time
evolution/distribution of RMSD, yet I see the opposite, apparently. What
does it mean?
Thanks,
Massimo
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